Originally, the area of the later remand prison at Genslerstrasse 66 housed a large canteen for the National Socialist People’s Welfare Organisation (NSV). Construction of this red-brick building was completed in 1939. In May 1945, the building was taken over by the Soviet occupying forces and turned into a prison camp known as "Special Camp No.3". This detainment and transit camp was directly controlled by the Moscow People's Commissariat for Internal Affairs (NKVD). From here, more than 20,000 prisoners were transported or forced marched to other Soviet camps including, for example, the former Nazi concentration camp at Sachsenhausen.

The living conditions in the camp were catastrophic. At times there were more than 4,200 people crammed together in a relatively small space. The food supplies were completely inadequate and the hygienic conditions appalling. Winter imposed an additional burden on the prisoners, with the cold so intense in the unheated cells that many became severely ill or died. Official Soviet statistics only list 886 mortalities here between July 1945 and October 1946, although estimates put that figure at over 3000. The bodies were disposed of at a refuse tip in bomb craters in the vicinity of the camp.

Most prisoners had been sentenced under the Soviet directive 00315, issued on April 18, 1945, which gave the authorities powers to seize and imprison spies, saboteurs, terrorists, Nazi party activists, members of the police and secret service, government officials, and other "hostile elements" in Germany. Later, the Soviets justified the wave of imprisonments by appealing to the August 1945 Allied agreement on finding influential Nazi sympathisers and arresting ex-Nazi officials in high administrative posts. However, many people the Soviets arrested had only been marginally involved in the Nazi system, if at all. Hence, the detainees not only included numerous non-ethnic Germans (above all, exile Russians) but also women and adolescents. Frequently, imprisonment was due to denunciation as was the case for the renowned German actor Heinrich George, incarcerated here before being transferred to Sachsenhausen where he died shortly afterwards. But critics of Soviet occupation ended up in Hohenschönhausen as well – as did, for instance, Karl Heinrich, SPD party member and commander of the Berlin Police force, who died in the camp at the end of 1945. In October 1946, Special Camp No. 3 was finally closed, not least because of the growing concern voiced by the local population. The prisoners were then relocated to other camps.

The Soviets set up a total of ten Special Camps in Germany and made Genslerstrasse the headquarters for their administration. The official – incomplete – statistics listed 122,000 Germans as held in these camps and, of these, more than a third died during imprisonment. The majority of those imprisoned were held for years without ever appearing before a court. From 1947 on, growing numbers of inmates had been sentenced by Soviet Military Tribunals (SMT). For example, in the former Special Camp etc. more than 12,000 German civilians were incarcerated in this way, with many of them accused of what was termed counter-revolutionary crimes. The last three camps – including the former Nazi concentration camp at Buchenwald – were only closed in early 1950, along with the Hohenschönhausen administrative headquarters.